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NM_020822.3(KCNT1):c.3281C>T (p.Thr1094Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Aug 14, 2020
Accession:
VCV000473384.8
Variation ID:
473384
Description:
single nucleotide variant
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NM_020822.3(KCNT1):c.3281C>T (p.Thr1094Met)

Allele ID
459716
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.3
Genomic location
9: 135786300 (GRCh38) GRCh38 UCSC
9: 138678146 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.138678146C>T
NC_000009.12:g.135786300C>T
NG_033070.1:g.89116C>T
... more HGVS
Protein change
T1094M, T1049M
Other names
-
Canonical SPDI
NC_000009.12:135786299:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00004
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00009
The Genome Aggregation Database (gnomAD), exomes 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00016
Links
ClinGen: CA5327766
dbSNP: rs373041291
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Aug 1, 2019 RCV000727041.3
Uncertain significance 1 criteria provided, single submitter Aug 14, 2020 RCV000544735.4
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV000592097.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNT1 - - GRCh38
GRCh37
1216 1274

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000726315.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Uncertain significance
(Jan 16, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000705105.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Aug 14, 2020)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, 5
Early infantile epileptic encephalopathy 14
Allele origin: germline
Invitae
Accession: SCV000652945.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces threonine with methionine at codon 1094 of the KCNT1 protein (p.Thr1094Met). The threonine residue is weakly conserved and there is a … (more)
Uncertain significance
(Aug 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001248980.6
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KCNT1 - - - -

Text-mined citations for rs373041291...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021